Kavyashree M wrote:
Dear Sir,
What does gmxcheck tell you about the .edr file that is giving weird
results? Do the plots look normal? Perhaps a frame got corrupted
somewhere along the way. The screen output should print how many
frames were considered in the analysis; if it does not match your
expectations based on nstenergy and the length of the simulation
then something went wrong.
gmxcheck gave proper number of frames corresponding to 100ns, other plots
temp, pressure, volume, density look fine
Most analyses do not need re-imaging. Keeping the protein within
the confines of one unit cell is typically just a convenience for
visualization.
Ok.
I had done simulations of four similar protein using the same mdp file.
in one of them
the minimum distance between the periodic images went near 0.9nm, I had
used 1.0nm
as distance between protein atoms and box wall. and cut offs were 1.0nm
for vdw and 1.4nm
for columb. Till some 17ns the minimum distance was above 2nm the
gradually there was a
dip after around 20-25ns. Now I ran 100ns simulation and I have to
discard this trajectory
because of this error. I thought distance of 2nm between protein atoms
was enough as 1.4nm
was the max cutoff.
How can we know prior to starting the simulation that we may get some
such errors for using
such a parameter. I could have used larger box size but it will increase
the time. Is it trial and
error basis to find out the optimum box size?
Generally, no, you don't have to waste lots of time fiddling with the box size
before you find the right one. The choice is based on the cutoffs and the
nature of the system. For a well-folded, stable protein, I see no reason why
what you've done isn't appropriate (unless you've set up the box incorrectly and
only think you've set certain dimensions). For disordered proteins or those
capable of large conformational changes, then the box needs to be large to
accommodate these possible motions.
The only other possibility I can think of is that the starting configuration
compressed a lot over time, shrinking the box. I don't know why this would
happen for a protein in water, but I suppose anything is possible. Most
condensed phase systems should not be very compressible, but any such change
would be obvious from plotting the volume over time. If it is stable, then the
protein must be doing something unexpected.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
